IGVFDS8557UXEJ

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS8557UXEJ/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS8557UXEJ",
    "aliases": [
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR1-Rep1_S121",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR2-Rep1_S127",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR3-Rep1_S175",
        "jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR4-Rep1_S181"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS8557UXEJ](/auxiliary-sets/IGVFDS8557UXEJ/) has sequence file(s) [IGVFFI3665MLGM](/sequence-files/IGVFFI3665MLGM/), [IGVFFI2578WMMF](/sequence-files/IGVFFI2578WMMF/), [IGVFFI1790WPVC](/sequence-files/IGVFFI1790WPVC/), [IGVFFI3467MIOR](/sequence-files/IGVFFI3467MIOR/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS8557UXEJ/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG011972/",
        "component": "functional characterization",
        "contact_pi": {
            "@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
            "title": "Jesse Engreitz"
        },
        "title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
    },
    "control_for": [],
    "creation_timestamp": "2024-05-14T16:24:18.255872+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO0384OZRW/",
            "accession": "IGVFDO0384OZRW",
            "aliases": [
                "igvf:donor_of_HCT116"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "gRNA sequencing",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI3665MLGM/",
            "accession": "IGVFFI3665MLGM",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR1-Rep1_S121"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:52:06.950336+00:00",
            "file_format": "fastq",
            "file_size": 26786723,
            "href": "/sequence-files/IGVFFI3665MLGM/@@download/IGVFFI3665MLGM.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/ac82b965-f1a5-4fd2-a996-cd9f362d7083/IGVFFI3665MLGM.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinA-PCR1-Rep1_S121_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI6081UZGH/",
            "accession": "IGVFFI6081UZGH",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR1-Rep1_S121"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:42:46.451287+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI6081UZGH/@@download/IGVFFI6081UZGH.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/b5058077-69f4-46a8-8635-f7cbb7903976/IGVFFI6081UZGH.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinA-PCR1-Rep1_S121.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2578WMMF/",
            "accession": "IGVFFI2578WMMF",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR2-Rep1_S127"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:52:25.066769+00:00",
            "file_format": "fastq",
            "file_size": 33392181,
            "href": "/sequence-files/IGVFFI2578WMMF/@@download/IGVFFI2578WMMF.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/5bc419ed-8f8a-4561-ac19-7a6ec211cc9a/IGVFFI2578WMMF.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinA-PCR2-Rep1_S127_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1790WPVC/",
            "accession": "IGVFFI1790WPVC",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR3-Rep1_S175"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:52:43.108337+00:00",
            "file_format": "fastq",
            "file_size": 29186941,
            "href": "/sequence-files/IGVFFI1790WPVC/@@download/IGVFFI1790WPVC.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/beefd2e9-4fba-4d73-9a37-cf23e8e5f6e9/IGVFFI1790WPVC.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinA-PCR3-Rep1_S175_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3467MIOR/",
            "accession": "IGVFFI3467MIOR",
            "aliases": [
                "jesse-engreitz:auxiliary_file_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR4-Rep1_S181"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-06-01T01:53:01.391441+00:00",
            "file_format": "fastq",
            "file_size": 45919416,
            "href": "/sequence-files/IGVFFI3467MIOR/@@download/IGVFFI3467MIOR.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/06/01/9ea2cfd3-e629-4a44-afaa-2dc1906cfcd2/IGVFFI3467MIOR.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0008565/",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220308B014_CCND1_SSFA2_FAM3C/fastq_trim/FAM3C-Auxin0hrs-FF2-BinA-PCR4-Rep1_S181_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI9888WBKI/",
            "accession": "IGVFFI9888WBKI",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR2-Rep1_S127"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:43:00.223195+00:00",
            "file_format": "yaml",
            "file_size": 914,
            "href": "/configuration-files/IGVFFI9888WBKI/@@download/IGVFFI9888WBKI.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/f2cfbda7-8baa-4d3e-be49-d0419960fa82/IGVFFI9888WBKI.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinA-PCR2-Rep1_S127.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI9150PTBN/",
            "accession": "IGVFFI9150PTBN",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR4-Rep1_S181"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:43:27.814614+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI9150PTBN/@@download/IGVFFI9150PTBN.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/b782090b-a56d-4e21-9ca3-d210484484e3/IGVFFI9150PTBN.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinA-PCR4-Rep1_S181.yaml",
            "upload_status": "validated"
        },
        {
            "@id": "/configuration-files/IGVFFI8784VUEB/",
            "accession": "IGVFFI8784VUEB",
            "aliases": [
                "jesse-engreitz:seqspecfile_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR3-Rep1_S175"
            ],
            "content_type": "seqspec",
            "creation_timestamp": "2024-06-11T20:43:13.648745+00:00",
            "file_format": "yaml",
            "file_size": 913,
            "href": "/configuration-files/IGVFFI8784VUEB/@@download/IGVFFI8784VUEB.yaml.gz",
            "s3_uri": "s3://igvf-files/2024/06/11/cb07ef55-8bd8-4c61-9a66-2784d08095a3/IGVFFI8784VUEB.yaml.gz",
            "status": "released",
            "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.FAM3C_Auxin0hrs-FF2-BinA-PCR3-Rep1_S175.yaml",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS5239VQTN/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS0101WKZK/",
            "accession": "IGVFDS0101WKZK",
            "aliases": [
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR1-Rep1_S121",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR2-Rep1_S127",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR3-Rep1_S175",
                "jesse-engreitz:measurement_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR4-Rep1_S181"
            ],
            "preferred_assay_title": "CRISPR FlowFISH screen",
            "status": "released"
        }
    ],
    "release_timestamp": "2024-07-10T20:11:22.474625+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM1718NCDJ/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM1718NCDJ",
            "aliases": [
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR1-Rep1_S121",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR2-Rep1_S127",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR3-Rep1_S175",
                "jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin0hrs-FF2-BinA-PCR4-Rep1_S181"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS1891GTLU/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
                    "modality": "interference",
                    "status": "released"
                },
                {
                    "@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
                    "modality": "degradation",
                    "status": "released"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002824/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:HCT116"
                    ],
                    "status": "released",
                    "summary": "HCT116",
                    "term_name": "HCT116"
                }
            ],
            "status": "released",
            "summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin A for 0-10% expression of FAM3C) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "12",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
        "title": "Chongyon Park"
    },
    "submitted_files_timestamp": "2024-06-01T01:52:06.950336+00:00",
    "summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "e7b5eb9e-7e1b-4ac3-a021-07306fe11297"
}